Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas

Abstract

Constitutional SMARCB1 mutations at 22q11.23 have been found in ∼50% of familial and <10% of sporadic schwannomatosis cases. We sequenced highly conserved regions along 22q from eight individuals with schwannomatosis whose schwannomas involved somatic loss of one copy of 22q, encompassing SMARCB1 and NF2, with a different somatic mutation of the other NF2 allele in every schwannoma but no mutation of the remaining SMARCB1 allele in blood and tumor samples. LZTR1 germline mutations were identified in seven of the eight cases. LZTR1 sequencing in 12 further cases with the same molecular signature identified 9 additional germline mutations. Loss of heterozygosity with retention of an LZTR1 mutation was present in all 25 schwannomas studied. Mutations segregated with disease in all available affected first-degree relatives, although four asymptomatic parents also carried an LZTR1 mutation. Our findings identify LZTR1 as a gene predisposing to an autosomal dominant inherited disorder of multiple schwannomas in ∼80% of 22q-related schwannomatosis cases lacking mutation in SMARCB1.

Figure 1

Distribution of mutations identified in the LZTR1 gene in individuals with schwannomatosis. Top, locations of frameshift, splice-site and missense mutations. Exons, introns and 5′ and 3′ UTRs are indicated by thick, thin and gray segments, respectively. Middle, LZTR1 protein domains and the locations of the genomic sequences encoding them (dotted lines): K-I–K-VI, Kelch motifs of the Kelch domain; BTB-I and BTB-II, BACK-I and BACK-II (partial BACK) domains. Bottom, missense mutations and the evolutionary conservation of the affected amino acids across ten different species up to the fruit fly. Blue, amino acids conserved up to the fruit fly; green, amino acids conserved up to the puffer fish. Recurrent p.Arg688Cys alterations were found in two unrelated individuals. An accession code for the GenBank protein record is given in parentheses for each species. See also Table 1.

Figure 2

Structural domains of LZTR1 and spatial predictions for missense alterations. Top left, structural modeling of a single Kelch motif and the predicted locations of missense alterations, as well as the entire Kelch domain consisting of six Kelch motifs (K-I to K-VI). Top right, structural modeling of dimeric and monomeric BTB domains (along with sequential distribution of α helices and β sheets) and the predicted locations of missense alterations in the BTB-I and BTB-II domains. Bottom, distribution and predicted locations of missense alterations.

Figure 3

Pedigrees of families positive for LZTR1 mutation with information from relatives available for testing. Filled symbols represent individuals clinically affected by schwannomatosis. Open symbols with a vertical line represent clinically asymptomatic, (likely) non-penetrant individuals carrying the familial LZTR1 mutation. Plus and minus signs indicate individuals positive or negative for the family-specific mutation, respectively. LZTR1 mutation in probands (arrows) was initially identified by next-generation sequencing of evolutionarily conserved sequences at 22q (NGS2, NGS3, NGS5, NGS7) or by sequencing the entire coding sequence of the LZTR1 gene and flanking intronic sequences (S1, S3, S6, S7, S9). Relatives were subjected to targeted analysis of the family-specific LZTR1 mutation identified in the proband.